Identification Of Papaya RLK Gene Family And Functional Differentiation Analysis Of Replicating Genes

Receptor-like kinases(RLK)are a large family of genes that are widely involved in regulating plant growth,stress response,and signal transduction in plants.The papaya genome consists of nine pairs of chromosomes(2n=18)and has a relatively small genome(approximately 372 Mb).At the same time,papaya has a fast growth rate,short generation(9-15 months),continuous flowering throughout the year,young sex chromosomes and a mature genetic transformation system,making it an advantageous material for molecular genetic breeding in fruit trees.In this study,we performed a genome-wide analysis of the RLK gene family and the LysM-RLK family in papaya(Carica papaya L.)using a bioinformatics approach.Currently,systematic studies on the RLK gene family and LysMRLK family have been focused on the model plants Arabidopsis thaliana and rice,but they have not been studied in papaya.The identification and analysis of the RLK gene family and LysM-RLK family in the papaya plant genome will help to improve the functional and evolutionary information of the RLK gene family and LysM-RLK family.In this paper,we used bioinformatics methods to identify the RLK gene family and LysM-RLK family in the genome of papaya by using the latest gene and protein sequences of Arabidopsis thaliana as materials,so as to obtain more complete information on the RLK family of papaya.At the same time,the classification,physicochemical properties,gene structure,evolution,gene duplication and functional differentiation of the family members were comprehensively analyzed to lay the informatics foundation for the next in-depth study of the RLK gene family.The main findings of this paper are as follows:1.Preliminary identification of RLK family by RGAs database and structural do main matching of genes of papaya in the existing database according to the classific ation of structural domains in Pfam database,RLK gene family was identified and a total of 378 RLK type genes were obtained.2.Gene structure prediction and motif prediction were performed for the 378 RLK genes identified,and inferred that insertions,deletions and differences in the number of motifs in their CDS regions may cause gene function differentiation.3.Multiple sequence alignment of protein sequences of the RLK gene family was performed using the software Muscle,and IQ tree software was used to constructan evolutionary tree.iTAK was used to classify the subclades of the evolutionary tree,and a total of 378 RLK family genes were classified into 62 subclades.4.After quality control,the transcriptional raw sequencing data collected from NCBI(Transcriptome data related to disease resistance,stress resistance,different tissues,and developmental processes)were matched to the reference genome using HISAT2,and then the reads were assembled using String Tie.The two pairs of gene pairs with significant expression were selected and validated for functional differentiation.5.Expression analysis was performed on the two pairs of candidate genes obtained from the screening,and the results showed that there were differences in homologous genes in response to drought stress,and functional differentiation might occur.6.Identification of the LysM-RLK gene family yielded seven papaya LysM-RLK family genes,and evolutionary analysis showed that the seven LysM-RLK genes of papaya could be divided into three subgroups(Lym-II,Lym-III,Lym-IV)and distri buted on four chromosomes.Gene duplication is the main driver of the evolution of the LysM-RLK subfamily in papaya,and gene duplication analysis identified seven pairs of duplicated genes.7.Analysis of the regulatory elements of the promoter sequence revealed that it contains several light-responsive elements and elements involved in low-temperaturer esponse and stress-related hormone signaling response.8.Large-scale comparative transcriptome analysis systematically resolved the gene expression patterns of LysM-RLK under biotic and abiotic stress conditions and in different tissues of papaya,revealing their specific expression patterns and potential biological functions.The expression differentiation of replicated gene pairs,structural domain composition differences and changes in protein tertiary structure implied its subfunctionalization during the evolutionary process.Core co-expression network ana lysis under biotic and abiotic stress conditions identified 27 core genes strongly asso ciated with LysM-RLK3,revealing the potential transcriptional regulation pattern of LysM-RLK3.The results provide important insights into the evolution of the LysMRLK subfamily origin and functional differentiation of papaya and its role in respon se to stress and during growth and development.